Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaatttcagttcctgatcaattttcgatcttacacttatcttaccagtgtattcttttcttttttttaatctattgattttcgttctgggagtgttgtgtgtttgcgatgtgtcacaatgtttagacaataataattctcatactgtaagtttgacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAACTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGT

Basic information

species Glycine max
transcript GLYMA10G30220.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30220.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G04870.2 (Arabidopsis thaliana), 3'ss of exon 2
gtttgtaatttcagttcctgatcaattttcgatcttacacttatcttaccagtgtattcttttcttttttttaatctattgattttcgttctgggagtgttgtgtgtttgcgatgtgtcacaatgtttagacaataataatt-ctcatactgtaagtttgacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAACTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGT
                                                                  |||  |  | |    |  ||  ||||     | |  |   |||  |  |  ||   ||  ||   ||    | | |  | | |  ||  | ||   |   |||| ||||| ||||| |||||||| || |||| ||  ||    ||||| || |||||||| || ||||| ||||||||||||||||||||||| ||||| ||
----------------------------------------------------------------ggtttcatgttatgagaagctttcttct-----tctaataattttctggagcatcgtgattcttgatcatctcttactgtttaaatggtctggttatgaatacagCTCCAAAGGGGTTATTTCCTCCAGAGCCTGTACCATACAAGGGACCTAAGCTGAAAGTAGCCATTATAGGAGCTGGACTTGCAGGCATGTCGACTGCTGT

upper sequence: GLYMA10G30220.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0030g01740.t01 (Vitis vinifera), 3'ss of exon 1
gtttgtaatttcagttcctgatcaattttcgatcttacacttatcttaccagtgtattcttttcttttttttaatctattgattttcgttctgggagtgttgtgtgtttgcgatgtgtcacaatgtttagacaataataattctcatactgtaagtttgacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAACTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGT
                                                                  |||||  | || ||   ||||  | |  |  ||   | |    ||  || |     ||  || ||   |    ||||| | | || | ||||| | || |||| ||||||||||||||||| || ||||||||||| ||| | |||||||| || || ||||| || ||||||||||| |||||||||||||||||||||||
----------------------------------------------------------------aatttttgtacctttttcctttcaatgtaagtttgaaatttagcagctctgaggtgttattattcgat--ttgcgattcttaaa-tggatgtttg-cttgccagCTCCAAAAGGGTTGTTTCCACCAGAACCTGAACACTATAGGGGACCAAAGCTCAAGGTGGCTATCATTGGAGCTGGGCTTGCAGGCATGTCAACTGCAGT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|192300731|gb|FG991113.1|FG991113
EST:     TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACG                         CGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAAC
genomic: TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACGgtttgtaatt ... gacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAAC
EST: gi|213589825|gb|DB969618.1|DB969618
EST:     TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACG                         CGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAAC
genomic: TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACGgtttgtaatt ... gacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAAC
EST: gi|151401347|gb|EV271161.1|EV271161
EST:     TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACG                         CGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAAC
genomic: TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACGgtttgtaatt ... gacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAAC
EST: gi|208074353|gb|GD868718.1|GD868718
EST:     CGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACCG                         CGCCAAA-GGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCA
genomic: CGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAAC-Ggtttgtaatt ... gacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCA
EST: gi|208300326|gb|GE100175.1|GE100175
EST:     TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACG                         CGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGA
genomic: TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACGgtttgtaatt ... gacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGA
EST: gi|208320445|gb|GE122460.1|GE122460
EST:     GCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGACGTTAAACG                         CGCCAAAAGGGTTGTTT
genomic: GCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAG-CGTTAA-CGgtttgtaatt ... gacatggcagCGCCAAAAGGGTTGTTT
EST: gi|209717713|gb|BW671531.1|BW671531
EST:     TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACG                         CGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAAC
genomic: TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACGgtttgtaatt ... gacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAAC
EST: gi|209702720|gb|BW652763.1|BW652763
EST:     TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACG                         CGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAAC
genomic: TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACGgtttgtaatt ... gacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAAC
EST: gi|192300798|gb|FG989710.1|FG989710
EST:     TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACG                         CGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAAC
genomic: TCGCCTTCGCTGCTCCTTAGATGCTAATGTTTCCGACATGAGCGTTAACGgtttgtaatt ... gacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtcacaatgtttagacaataataattctcatactgtaagtttgacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAACTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGT
                                         gtttgac  putative branch site (score: 4)
        aatgtttagacaataa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtaatttcagttcctgatcaattttcgatcttacacttatcttaccagtgtattcttttcttttttttaatctattgattttcgttctgggagtgttgtgtgtttgcgatgtgtcacaatgtttagacaataataattctcatactgtaagtttgacatggcagCGCCAAAAGGGTTGTTTCCTCCGGAACCTGAACATTATCGAGGACCAAAACTGAAAGTGGCAATTATTGGAGCTGGACTTGCAGGCATGTCAACTGCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG